Suzanne de Bruijn

296 Chapter 6 Proteomics and metabolomics The integration of proteomics or metabolomics studies with genomics has been less well studied, which can mostly be attributed to the complexity of the corresponding analyses. Whereas proteomics focuses on studying changes at the proteome level (e.g. aberrant protein structure or overexpression), metabolomics can be employed to detect changes in metabolite composition (e.g. lipids, sugars or amino acids). Recently, a first study was reported, employing a combined genomics, transcriptomics and proteomics approach using fibroblast cells in a diagnostic setting for cases suspected to suffer from a mitochondrial disease. 85 Independent cumulative evidence was derived from the three techniques and a success rate of 21% was reached using the combined approach. In general, mitochondrial dysfunction is known to significantly affect cell metabolism for which the consequences can be relatively easily detected in a proteomics approach. Considering the immune-privileged nature of the eye and the ear, it is less plausible that proteomic or metabolic abnormalities caused by RD or HL-associated genetic defects, can be detected in readily accessible cells or tissues such as fibroblast and blood ( Box 1 ). Therefore, the implementation of proteomics or metabolomics in HL- and RD- diagnostics is likely to be less effective. Nevertheless, in case of syndromic phenotypes that include both mitochondrial dysfunction and HL or RD, success stories have been described (e.g., CLN3 implicated in lethal, syndromic RD (Batten disease) and RMND1 in syndromic HL with chronic kidney disorder). 86,87 Therefore, a combined genomics and proteomics or metabolomics approach should not be completely discarded and could still be considered dependent on the patient’s phenotype. Epigenomics Epigenomic studies can be performed to make an inventory of chromatin modifications (epigenetic hallmarks), to reveal active regulatory elements, or the 3D chromosome organization (chromosome conformation capture techniques). The presence or absence of chromatin modifications that are associated with active cis regulatory elements (e.g. H3K27Ac, chromatin accessibility and transcription factor binding) can be explored with a variety of techniques such as chromatin immunoprecipitation (ChIP)-sequencing, an assay for transposase accessible chromatin (ATAC)-sequencing, and DNase I hypersensitive sites (DNase)-sequencing. However, these methods require millions of cells as input material. A recently developed Cleavage Under Targets and Tagmentation (CUT&Tag) protocol allows high-resolution profiling of important epigenetic hallmarks in a single-tube experiment. 88 This makes it possible to perform epigenomic profiling in small samples and even single cells, which is of particular interest for tissues and cell-types with limited availability as is the case for both the inner ear and the retina ( Box 1 ). Pathogenic regulatory variants could have an effect on transcription factor